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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data_1 when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-09-28, 19:38 based on data in: /home/qinchunyuan/proteomicsDIA/mzml/pmultiqc_test


        pmultiqc

        pmultiqc is a multiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms.

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.

        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 4/4 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        SWATH-TN-10-1.wiff.mzML3112
        breast cancer
        2
        SWATH-TN-10-2.wiff.mzML4112
        breast cancer
        2
        SWATH-TN-9-1.wiff.mzML1111
        breast cancer
        1
        SWATH-TN-9-2.wiff.mzML2111
        breast cancer
        1

        Summary Table

        This table shows the quantms pipeline summary statistics

        This table shows the quantms pipeline summary statistics

        Showing 1/1 rows and 2/2 columns.
        #MS2 Spectra#Peptides Quantified#Proteins Quantified
        534120
        19163
        3629

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 4/4 rows and 7/7 columns.
        Spectra FileSample NameConditionFraction#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
        SWATH-TN-10-1.wiff.mzML
        2
        breast cancer
        1
        9270
        9270
        0
        3379
        SWATH-TN-10-2.wiff.mzML
        2
        breast cancer
        1
        11046
        11046
        0
        3706
        SWATH-TN-9-1.wiff.mzML
        1
        breast cancer
        1
        12771
        12771
        0
        3952
        SWATH-TN-9-2.wiff.mzML
        1
        breast cancer
        1
        14471
        14471
        0
        4440

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

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        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

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        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

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        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

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        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        ASSEMBLE_EMPIRICAL_LIBRARY DIA-NN 1.8.1
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DIANNCFG sdrf-pipelines 0.0.21
        DIANNCONVERT pmultiqc 0.0.13
        DIANN_PRELIMINARY_ANALYSIS DIA-NN 1.8.1
        INDIVIDUAL_FINAL_ANALYSIS DIA-NN 1.8.1
        MZMLINDEXING FileConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        friendly_edison
        containerEngine
        singularity
        launchDir
        /hps/nobackup/juan/pride/reanalysis/dia-projects/PXD014194
        workDir
        /hps/nobackup/juan/pride/reanalysis/dia-projects/PXD014194/work
        projectDir
        /hps/nobackup/juan/pride/reanalysis/quantms
        userName
        pst_prd
        profile
        ebiclusters
        configFiles
        /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config, /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config

        Input/output options

        input
        PXD014194.sdrf.tsv
        outdir
        PXD014194
        email
        yperez@ebi.ac.uk
        root_folder
        /hps/nobackup/juan/pride/reanalysis/dia-projects/PXD014194/

        Protein database

        database
        /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-isoforms-contaminants-202105.fasta

        Database search

        allowed_missed_cleavages
        1
        instrument
        N/A
        max_mods
        1

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        1

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        skip_post_msstats
        true
        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Max job request options

        max_cpus
        48
        max_memory
        300 GB
        max_time
        10d

        Generic options

        email_on_fail
        yperez@ebi.ac.uk
        hostnames
        N/A